Aim

  • Learn about packages in R
  • Use Bioconductor

Packages

Packages are collection of several functions in R.

To use a perticular function from a package, it need to be downloaded and loaded.

Introduction to Bioconductor

Bioconductor is a collection of more than 1,500 packages for the statistical analysis and comprehension of high-throughput genomic data. Originally developed for microarrays, Bioconductor packages are now used in a wide range of analyses, including bulk and single-cell RNA-seq, ChIP seq, copy number analysis, microarray methylation and classic expression analysis, flow cytometry, and many other domains.

This session introduces the essential of Bioconductor package discovery, installation, and use.

Use Biocondutor

Discovering, installing, and learning how to use Bioconductor packages.

The web site at https://bioconductor.org contains descriptions of all Bioconductor packages, as well as essential reference material for all levels of user.

Usecase

Lets see how to do diffrential expression analysis using Biocondutor package called DESeq2

Get the required files using wget in terminal.

This above is derived from Bioconductor experimental data airway package. Which is a part this publication.

General commands to run DESeq2

Key Points

  • To install packages from Biocondutor BiocManager::install(pkg_name)
 

Created and Maintained by Sangram Keshari Sahu
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